A prototype multiped tank has destroyed two other prototypes and broken out of a testing facility. Section 9, employing its own smaller multiped, the Tachikomas, is brought in to stop it.

The hijacker is using the ID of the tank's designer who had recently died. Whoever is operating the tank, their motives are unknown. Section 9 has little time to figure out these two mysteries before the tank enters the urban area.

While tracking the New World Brigade, an anti-cyberization group, to an unused radiation scrubber facility off Okinawa, the Japanese Maritime Safety Agency took pictures that show Eka Tokura, the kidnapped daughter of a cyber-technology company CEO. However, the girl had been abducted over 16 years ago when she had been 10 years old. In the recent photos, she looks just as she did on the day she was taken.

For reasons unknown, contact with the Maritime Safety Agency's reconnaissance team has been lost. Section 9 heads to the facility to locate the unit and find out why Eka Tokura was there.

Togusa has been released from jail, but his badge and gun are confiscated and he is given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but turns up nothing.

Trying to turn his life around, he begins to look for a new job, only to be sidetracked by the ongoing case against Secretary-General Yakushima involving the illegal use of micromachines. With the news plastered everywhere, Togusa cannot help but wonder where he stands now.

Armed terrorists have taken over the Chinese Embassy in New Port City. Holding an unknown number of hostages, the group, calling themselves the Individual Eleven, are demanding that the government cease accepting Asian refugees and dissolve the five Asian refugee camps situated throughout Japan.

The members of Section 9 have mobilized and are in position to move in. However, due to the events of the Laughing Man Incident (1st GIG), Section 9 technically no longer exists. The unit must wait for an official order from Chief Aramaki, who is busy making his case in front of the new Prime Minister of Japan.

Several bombings have occurred throughout New Port City. Each time, Section 9 arrives too late to stop their detonations. With a fifth and final bomb set to go off somewhere in the city, the unit puts all of the information they have found from the first four bombings together.

Even the Cabinet Intelligence Service is having their fair share of difficulties. A hacker has infiltrated its incredibly advanced computer security system. The hacker enters the vast array of information stored at the CIS and begins to collect data...

The Chief Cabinet Secretary uses the excuse of the refugees possessing 10kg of plutonium to mobilize the military against Dejima. With the available evidence against the refugees, Prime Minister Kayabuki reluctantly agrees. However, she soon learns from the Chief Cabinet Secretary that he's aligned himself with Imperial America and is now after her job.

Knowing her days as P.M. are numbered, she agrees with Aramaki's plan and calls the U.N. in for a nuclear inspection of Dejima. The move buys them some time to defuse the situation, and Section 9 heads to Dejima to meet up with the U.N in two days. However, with tensions running high it is only a matter of time before someone fires the first shot.

Kuze and the Major come up with a plan to save the refugees, but the chances of its success are slim. Realizing this, the Tachikomas disobey the Major's orders and come up with a plan of their own. Batou has also disobeyed the Major's orders to go to the bridge and is desperately searching for her in the ruins of Dejima. Meanwhile, the Prime Minister is frustrated with being spurned by the Chief Cabinet Secretary. Determined to be remembered as more than a mere figurehead, she takes matters into her own hands.